CHEM204: Bioorganic Chemistry

Unit 2: BiomoleculesBiomolecules are organic molecules synthesized in living organisms.
All biomolecules are organic, meaning that they are primarily composed
of carbon, hydrogen, nitrogen, and oxygen. Some biomolecules contain
other atoms as well (e.g. phosphorus and/or sulfur). Biomolecules vary
in size. Some are large polymeric molecules, such as proteins,
polysaccharides, and nucleic acids, while others are small, such as
metabolites, lipids, and the monomers of the polymers.

In Organic Chemistry, you learned about organic compounds; this unit
will focus on carbohydrates, lipids, amino acids, and nucleic acids that
occur in the cell. In Organic Chemistry, you also learned about
stereoisomerism; this unit will focus on stereoisomers that are produced
by the cell, including chiral molecules and cis-trans isomers. You may
recall that some reactions involving organic compounds produce specific
stereoisomers. The stereoselectivity of reactions in the cell is more
pronounced, because enzymes that catalyze biochemical reactions are
chiral themselves. Only one enzyme enantiomer exists in the cell and
has biological activity. Life on Earth is chiral.

Unit 2 Time Advisory
This unit should take you approximately 30.75 hours to complete.

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Subunit 2.1: 4 hours
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Subunit 2.1.1: 2 hours

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Subunit 2.1.2: 1 hour

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Subunit 2.1.3: 1 hour

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Subunit 2.2: 3.75 hours
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Subunit 2.2.1: 1.75 hours

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Subunit 2.2.2: 2 hours

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Subunit 2.3: 8 hours
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Subunit 2.3.1: 3.5 hours

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Subunit 2.3.2: 2 hours

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Subunit 2.3.3: 2 hours

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Subunit 2.3.4: 0.5 hour

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Subunit 2.4: 5.25 hours
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Subunit 2.4.1: 2.5 hours

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Subunit 2.4.2: 2.75 hours

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Subunit 2.5: 3 hours

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Subunit 2.6: 6 hours
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Subunit 2.6.1: 2.25 hours

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Subunit 2.6.2: 1 hour

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Subunit 2.6.3: 2.75 hours

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Subunit 2.7: 0.75 hour

Unit2 Learning Outcomes
Upon successful completion of this unit, the student will be able to:
- Identify and characterize lipids, carbohydrates, amino acids, and
nucleic acids.
- Recognize chiral organic molecules, and explain their biological
significance.
- Recognize cis-trans isomers, and explain their biological
significance.
- Compare and contrast the progress of chemical reactions with and
without catalysis.
- Define the function of coenzymes.
- Design enzyme catalyzed reactions leading to high-energy compound
products.

Instructions: Please click on the link above, and take notes as you
watch the video (7 minutes). Listen the presentation carefully two
or three times as needed until you are able to explain what
chirality is and also how to recognize a chiral molecule. Note that
chirality rests on the presence of at least one carbon atom, which
binds to four different functional groups.

Viewing this lecture several times and pausing to take notes should
take approximately 30 minutes to complete.

Instructions: Please click on the links above, and take notes as
you watch the videos (12 minutes and 11 minutes respectively).
Listen to the presentation carefully two or three times as needed,
and practice how to recognize a chiral molecule by working through
the examples provided in the video lectures.

Viewing these lectures several times and pausing to practice the
identification of chiral molecules should take approximately 1 hour
to complete.

Instructions: Please click on the link above, and on a separate
piece of paper,answer all of the quiz questions in the “Chiral or
Optical Isomers” column of the table. Then, click on the drop-down
menu next to each question to check your answers. Note that chiral
compounds are also called “optical isomers” or “optically active”
substances, because the isomers have the ability to rotate the plane
of the polarized light. Optical activity is measured with
polarimeter, and some microscopes are equipped with polarimeter.

This assessment will take approximately 30 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and take notes as you
watch the video (14 minutes). Listen to the presentation carefully
two or three times until you are able to explain what diastereomers
are and how to recognize a chiral molecule and a diastereomer. Note
that diastereomers include cis-trans isomers, non-enantiomeric
chiral compounds, and epimers; epimers have more than one chiral
center, but differ only in one chiral center (the others are
identical); and meso compounds have an internal plane of symmetry.

Viewing this lecture several times and pausing to take notes should
take approximately 30 minutes to complete.

Instructions: Please click on the link above, and on a separate
piece of paper, answer all "Quiz" questions in the "Cis – Trans
Isomers of Alkenes" column of the table. Finally, click on the
drop-down menu next to each question to check your answers.

This assessment should take approximately 30 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and study this entire
webpage. Take advantage of the “Interactive Link Maps” at the
bottom of the page; in particular, make sure to select the links to
“First Level,” “Second Level,” and “Third Level.”

Studying this resource will take approximately 1 hour to
complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and on a separate
piece of paper, answer all quiz questions in the “Fatty Acids”
column of the table. Then, click on the drop-down menu next to each
question to check your answers.

This assessment will take approximately 15 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, scroll down to
“Prostaglandins Thromboxanes & Leukotrienes,” “Terpenes,” and
“Steroids,” and study these sections in their entirety. Select the
embedded “Click Here” links to examine lipid models. Also, click on
the grey “Toggle Structures” button to reveal the structural
formulas of additional lipids. Note that the arachidonic acid is an
ω-6 fatty acid; it is an essential fatty acid, which is the
precursor of prostaglandin and leukotriene production.

Studying this resource will take approximately 1 hour and 30
minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above,and on a separate
piece of paper, answer all of the quiz questions in the
“Prostaglandins” column of the table. Then, click on the drop-down
menu next to each question to check your answers.

This assessment will take approximately 15 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and on a separate
piece of paper,answer all of the quiz questions in the
“Prostaglandins” column of the table. Then, click on the drop-down
menu next to each question to check your answers.

This assessment will take approximately 15 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and study the “1.
Glucose” and “3. Ketoses” sections on this webpage. Please note the
number of optical hexose isomers, including diastereomers. Make
sure to click on any embedded links to read about associated
content.

Studying this resource will take approximately 1 hour and 30
minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please note that this assessment is optional. Please
click on the link above to access the assessment, and read the
instructions at the top of the webpage. Please click on a "Graphic"
link in the "Static Graphic Image" column; this will show you the
structural formula of a carbohydrate compound. Your task is to
recognize the compound. After you have identified the compound,
check your answer. The right answers are in the "Compound" column
of the table: click on the drop-down menu labeled "Answer" to reveal
the correct answer to the quiz question. Next, determine if the
structural formula is an alpha or a beta epimer. In the "Alpha or
Beta" column of the table, click on the drop down menu labeled
"Answer" to reveal the correct answer to the quiz question.

This assessment will take approximately 2 hours to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, scroll down to “4.
Anomeric Forms of Glucose,” “5. Cyclic Forms of Monosaccharides,”
and “6. Glycosides,” and study these sections on this webpage. Note
that the cyclic anomers are hemiacetals.

Studying this resource will take approximately 2 hours to
complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and study the four
diagrams and their descriptions in the “Sugar Derivatives” section.
Please note the substitutions in these sugar derivatives, and
investigate if these substitutions influence the number of chiral
carbon atoms in the molecule.

Studying this resource will take approximately 30 minutes to
complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, scroll down to “2.
Natural α-Amino Acids,” “3. The Isoelectric Point,” and "4. Other
Natural Amino Acids," and study these sections in their entirety.
Please locate the "Physical Properties of Selected Acids and
Amines" tablein the “2. Natural α-Amino Acids” section, and compare
the structures of tyrosine, cysteine, lysine, and aspartic acid.

Studying this resource will take approximately 2 hours to
complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and answer the
questions in the “Polar or Non-Polar” and “Acidic, Basic, or
Neutral” columns. Twenty amino acids are listed here, thus you have
to answer forty questions. Make sure that you answer each question
before you check the correct answer. Please write down your
responses. After you have identified each structure, you can check
whether your responses are correct by clicking on the drop-down
menus marked “Answer.”

This assessment will take approximately 30 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and study this entire
webpage. Next, follow the links at the bottom of this page to learn
“How Proteins Get Their Shape,” “Primary Structure,” “Secondary
Structure,” “Tertiary Structure,” and “Quaternary Structure.”
Please take advantage of the many embedded links on this page.

Studying this resource will take approximately 2 hours to
complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and complete all quiz
questions in the “Amino Acid Peptide Bonds” column. Please write
down the complete reaction or the reaction product as required
before checking the correct response. You can check whether your
responses are correct by clicking on the “Answer Graphic” link.

This resource will take approximately 30 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, scroll down to “2.
The Chemical Nature of DNA” and “4. The Secondary Structure of DNA,”
and study these sections on this webpage. Please note that the
backbone of the nucleic acid polymer is made of phosphodiester
bonds.

Studying this resource will take approximately 2 hours to
complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and complete "Problem
8: Complementary Bases.” Clicking on a response will lead you to a
tutorial page where your response will be accepted, if it is
correct. If you make a mistake, you will find a short explanation
on the page. In this case where you have selected an incorrect
answer, please return to the problem, and try answering the question
again.

This assessment will take approximately15 minutes to complete.

Terms of Use: Please respect the copyright ant terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and study the “3.
RNA, a Different Nucleic Acid” section on this webpage. Click on
the “Components of Nucleic Acids” table to reveal the structure of a
short RNA polymer.

This resource will take approximately 30 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and on a separate
piece of paper,complete the two quiz sections in the “DNA and RNA
Introduction” column. You can check whether your responses are
correct by selecting the “Answer” drop down menu.

This resource will take approximately15 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instruction: Please click on the link above, and study "The
Catalytic Activity of Enzymes,” the "Mechanisms of Enzymatic
Catalysis,” and the "Regulation of Enzyme Activity" sections on this
page. Please note that the "Coenzymes" section of this webpage will
be covered in Subunit 2.6.2.

Reading and note taking will take approximately 1 hour and 30
minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and complete the quiz
questions in the “Role of Enzymes in Biochemical Reactions” column.
Please write down your responses. You can check whether your
responses are correct by clicking on the drop-down menu “Answer”
boxes.

This assessment will take approximately 15 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and complete the quiz
questions in the “Enzyme Inhibitors” column. Please write down your
responses. You can check whether your responses are correct by
clicking on the drop-down menu “Answer” boxes.

This assessment will take approximately 30 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instruction: Please click on the link above, and study the
"Coenzymes" section on this page. Note that coenzymes are essential
for the activity of many enzymes. Please note that you have already
studied this webpage in Subunit 2.6.1, where you have focused on
general characteristics of enzymes. Enzymes are amino acid
polymers. In this Subunit, you learn about coenzymes, which are
small organic molecules. Coenzymes are essential for the biological
activity of certain enzymes. For example, nicotine adenine
dinucleotide (NAD+) is essential for the function of
alcohol dehydrogenase, which has a detoxification role in our body
after alcohol consumption. Many enzymes catalyze biological
reactions without needing a coenzyme, e.g. trypsin and chymotrypsin
work without coenzyme; these enzymes catalyze protein hydrolysis in
the small intestine.

This resource will take approximately 1 hour to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instruction: Please click on the link above, and study this entire
text. Please note that anabolic reactions invest energy into
building complex molecules, and this energy is provided by catabolic
reactions.

Reading and taking notes should take approximately 2 hours and 30
minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above, and complete the quiz
questions in the “Electron Transport” column. Please write down
your answers. You can check whether your responses are correct by
clicking on the drop-down menu “Answer” boxes.

This assessment should take approximately 15 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

Instructions: Please click on the link above to access the
assessment. You will find the structural formula of a biomolecule
in the center of the page and the names of 14 biomolecule groups on
the right side. Drag and drop the name of the biomolecule into the
black box under the structural formula. You will receive immediate
feedback. If your answer iscorrect,the next structural formula will
appear and you can choose again. If your answer is incorrect, then
you may try to answer the question again. You can also bypass a
structural formula if you do not know the answer by clicking on the
“Next” button, which appears at the top of the webpage above the
structural formula. This website has a large database, so expect to
see different structural formulas and several different structures
for the same compound groups.

This assessment will take approximately 45 minutes to complete.

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.